School of Natural Sciences, Department of Bioscience, TU Munich, D-85748Garching, Germany.
J Am Chem Soc. 2023 Jan 11;145(1):634-644. doi: 10.1021/jacs.2c11208. Epub 2022 Dec 26.
Toehold-mediated strand displacement (TMSD) has been used extensively for molecular sensing and computing in DNA-based molecular circuits. As these circuits grow in complexity, sequence similarity between components can lead to cross-talk, causing leak, altered kinetics, or even circuit failure. For small non-biological circuits, such unwanted interactions can be designed against. In environments containing a huge number of sequences, taking all possible interactions into account becomes infeasible. Therefore, a general understanding of the impact of sequence backgrounds on TMSD reactions is of great interest. Here, we investigate the impact of random DNA sequences on TMSD circuits. We begin by studying individual interfering strands and use the obtained data to build machine learning models that estimate kinetics. We then investigate the influence of pools of random strands and find that the kinetics are determined by only a small subpopulation of strongly interacting strands. Consequently, their behavior can be mimicked by a small collection of such strands. The equilibration of the circuit with the background sequences strongly influences this behavior, leading to up to 1 order of magnitude difference in reaction speed. Finally, we compare two established and one novel technique that speed up TMSD reactions in random sequence pools: a three-letter alphabet, protection of toeholds by intramolecular secondary structure, or by an additional blocking strand. While all of these techniques were useful, only the latter can be used without sequence constraints. We expect that our insights will be useful for the construction of TMSD circuits that are robust to molecular noise.
适体介导的链置换(TMSD)已广泛应用于基于 DNA 的分子电路中的分子传感和计算。随着这些电路变得越来越复杂,组件之间的序列相似性可能会导致串扰,从而导致泄漏、改变动力学特性甚至导致电路故障。对于小型非生物电路,可以针对这些不需要的相互作用进行设计。在包含大量序列的环境中,考虑所有可能的相互作用是不可行的。因此,深入了解序列背景对 TMSD 反应的影响具有重要意义。在这里,我们研究了随机 DNA 序列对 TMSD 电路的影响。我们首先研究了单个干扰链,并使用获得的数据构建了估计动力学的机器学习模型。然后,我们研究了随机链池的影响,发现动力学仅由一小部分强烈相互作用的链决定。因此,它们的行为可以由一小部分此类链模拟。电路与背景序列的平衡强烈影响这种行为,导致反应速度相差一个数量级。最后,我们比较了两种已建立的和一种新的技术,这些技术可以加快随机序列池中的 TMSD 反应:三字母字母表、通过分子内二级结构保护适体或通过附加的阻断链。虽然这些技术都很有用,但只有后者可以在没有序列限制的情况下使用。我们期望我们的见解将有助于构建对分子噪声具有鲁棒性的 TMSD 电路。